TPP:4.4.0 Release Notes

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Revision as of 18:17, 16 August 2010; view current revision
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To developers: I put this page in place to help manage the 4.4.0 "Vuvuzela" release. The punch list is a list of tasks/issues that need to be resolved for the list. I'll incorporate the known issues and the release notes into the final release bulletin. To facilitate the generation of the release notes I've captured all of the subversion change logs and sorted them by user. Please review your set of changes condense them into what you want to say about the changes for the release.

Known issues

XPressPeptideParser crash

>> When Brian
>> was working through testing for Chris P's code review, he had some
>> issues (unrelated to Chris) that showed some trunk issues.
Yeah, specifically what I found was that starting with Jimmy's change
4785 I get a crash in XPressPeptideParser with one of my smoketest
data sets, but only on my MinGW build (not MSVC, not linux), and not
in gdb (that last detail says "stack issue" to me).  Looking at the
changes in that commit I don't think it's anything Jimmy did, I think
that just happened to expose a latent stack issue which I've had no
luck tracking down.
>> Given that nobody else seems to have hit this I think we should just
>> let it ride.
Sorry, I meant 4782.  When I roll back to 4781 I don't get a crash,
when I go to 4782 I do.  But again, I can't see that it's anything you
did in that commit, and I can't repro inside gdb, or with MSVC under
any circumstance.

Brian

Release Notes

Trunk changes since revision 4498 (creation of 4.3 branch by spacepod)

cpaulse

r4974 | cpaulse | 2010-05-13 12:13:21 -0700 (Thu, 13 May 2010) | 1 line

fix tpp.sln for vc9

r4918 | cpaulse | 2010-03-29 14:33:30 -0700 (Mon, 29 Mar 2010) | 5 lines

Branch visual studio 8 tpp.sln file (and dependent vcproj files) to tppvc8.sln.

tpp.sln and dependent vcproj files converted to visual studio 2008 express, with atl/mfc dependent projects (mzwiff, trapper, masswolf, readw), msconvert, and pwiz_swig projects removed from tpp.sln (last two don't compile in 2008 express and have no internal dependencies). extern/build_boost_vc8.bat renamed.

minor bug fix to release configuration of readmzXML.vcproj.

r4917 | cpaulse | 2010-03-29 11:08:10 -0700 (Mon, 29 Mar 2010) | 2 lines

Fix reading of search engine specific input data where multiple search results are present for a single spectrum. Compile warning in Visual C++ (PhosphoMixtureDistr.cxx).

r4901 | cpaulse | 2010-03-12 08:51:32 -0800 (Fri, 12 Mar 2010) | 1 line

fix destructor semantics for iProphet

r4899 | cpaulse | 2010-03-10 12:04:17 -0800 (Wed, 10 Mar 2010) | 1 line

don't delete RT and PI mixtureDistr's twice.

r4898 | cpaulse | 2010-03-10 09:13:32 -0800 (Wed, 10 Mar 2010) | 1 line

fix memory leaks in PeptideProphetParser, and type cast warnings generated by visual studio in spectrast

r4890 | cpaulse | 2010-02-28 14:32:24 -0800 (Sun, 28 Feb 2010) | 1 line

undo my destruction of Peptide::mods semantics.

r4889 | cpaulse | 2010-02-26 11:35:58 -0800 (Fri, 26 Feb 2010) | 1 line

more missed files intended for changeset 4885

r4887 | cpaulse | 2010-02-26 11:19:01 -0800 (Fri, 26 Feb 2010) | 1 line

missed from changeset 4885

r4885 | cpaulse | 2010-02-25 15:21:11 -0800 (Thu, 25 Feb 2010) | 1 line

modernize integer definitions enough to stop visual studio 9 from issuing warnings at level 3.

real_procopio

pepXML schema

New pepXML 1.15: Adds more search engines (ProteinPilot, ProteinLynx, Spectrum Mill, greylag, Phenyx, Proteios, Crux, Tide) and activation methods (ETD/CID, HCD).

MzXML2Search

Added "mzML" to usage statement

Petunia

Moved mzXML utils to new tab
Changed wording on home page to state using mzML as the standard
Added indexmzXML page
Optionally authenticate against an .htpasswd entry (from J.Slagel)
Fix tabs (from 4.3 branch)

New options

PeptideProphet:
- Use Phospho model

XPRESS:
- Allow passing of negative mass offsets
- Min Points needed
- Sum N isotopic peaks)
MzXML2Search:
- Output N Top Peaks
- Max Charge State
- Output Precision
- Removed ion mass option

Technical changes:

Minor corrections to session handling
Add trailing slash to tppbin definition
Added a variable to hold location of tpp-bin
Refer to tpp_hostname by full path
Silence perl warning (more to go...)
Provide path to plotspectrast.cgi when calling Lib2HTML
Minor form closing changes to avoid mis-formatting in IE

xinteract

Adding isotopic peaks XPRESS option to usage statement

readmzXML

Add -r option to output spectrum data only; no title or extra CR's. (Replicates functionality of Jimmy's getSpectrum)

Pep3D

Enable viewing of MS2-only data (no elution, but at least you can see the distribution of sequencing events)
Larger input field for filename
Use dhtml to print/display messages (also simplify error messages so they display correctly).

plot-msms (spectrum viewer)

Added Image Size option
Update to unified look and feel

protxml2html (ProteinProphet viewer)

Add command-line usage statement
Took out a bunch of commented-out code.
Performance improvements:
- Define several 'global' variables in xsl to avoid costly lookups
- Add option not to generate Gaggle files

Limited testing gives speeds up to 5x faster than previous version.

dctrud

r4884 | dctrud | 2010-02-25 02:42:00 -0800 (Thu, 25 Feb 2010) | 1 line

[ASAPRatioProteinRatioParser] Implement PepXML cacheing as XPRESS

pcbrefugee

r5043 | pcbrefugee | 2010-06-24 08:22:26 -0700 (Thu, 24 Jun 2010) | 1 line

[Mascot2XML] fatal error messages about enzyme definition issues are always useful, ignore the state of verbose_ flag for these

r5036 | pcbrefugee | 2010-06-14 16:16:26 -0700 (Mon, 14 Jun 2010) | 1 line

[pwiz] sync up to latest from ProteoWizard, their rev 2047

r4995 | pcbrefugee | 2010-05-28 10:56:11 -0700 (Fri, 28 May 2010) | 1 line

[pwiz] get current with ProteoWizard codebase - sync to pwiz commit number 2005

r4992 | pcbrefugee | 2010-05-28 10:21:54 -0700 (Fri, 28 May 2010) | 1 line

[indexmzXML] light changes to accomodate ever-stricter GCC's handling of long long (it doesn't like that), also fix and off-by-one error that left the last entry in the index untested.

r4954 | pcbrefugee | 2010-04-20 13:12:51 -0700 (Tue, 20 Apr 2010) | 1 line

[various] add a bunch of missing initializations - stack and dynamically allocated memory cannot be expected to be zeroed out. Also, don't call delete on malloc'd memory, use free instead.

r4937 | pcbrefugee | 2010-04-09 17:03:15 -0700 (Fri, 09 Apr 2010) | 1 line

[MzXMLSearch] change a variable size stack allocation of peak structs to new/delete allocation (some older compilers don't like that syntax, and it risks stack overflow too)

r4935 | pcbrefugee | 2010-04-09 15:39:07 -0700 (Fri, 09 Apr 2010) | 1 line

[MzXML2Search] fix a crash when WEBSERVER_ROOT env variable isn't set

r4929 | pcbrefugee | 2010-04-06 12:50:50 -0700 (Tue, 06 Apr 2010) | 1 line

[Pepc] update GWT and GChart to current versions and tweak color select code to satisfy IE8

r4928 | pcbrefugee | 2010-04-05 15:07:46 -0700 (Mon, 05 Apr 2010) | 1 line

[pwiz] add a missing pwiz source file for ABI_T2D that was tripping up the xtandem build on linux

r4926 | pcbrefugee | 2010-04-01 10:28:53 -0700 (Thu, 01 Apr 2010) | 1 line

[pwiz] handful of pwiz files missed again(!) in the previous commit (something's up with my TortoiseSVN installation?)

r4925 | pcbrefugee | 2010-04-01 09:59:20 -0700 (Thu, 01 Apr 2010) | 1 line

[pwiz] handful of pwiz files missed in the previous commit

r4924 | pcbrefugee | 2010-04-01 08:34:04 -0700 (Thu, 01 Apr 2010) | 1 line

synch up to Proteowizard rev 1925

r4920 | pcbrefugee | 2010-03-30 16:11:50 -0700 (Tue, 30 Mar 2010) | 1 line

Finish various renames of VC8 project files for the VC8 build.

r4919 | pcbrefugee | 2010-03-30 15:57:47 -0700 (Tue, 30 Mar 2010) | 1 line

tidy up notes to match current code

r4914 | pcbrefugee | 2010-03-23 16:15:51 -0700 (Tue, 23 Mar 2010) | 1 line

tweaks for MSVC build

r4913 | pcbrefugee | 2010-03-23 15:41:24 -0700 (Tue, 23 Mar 2010) | 1 line

[PepC] allow more seperator types in CSV files (comma, tab, semicolon, colon, space) and properly handle error cases where none of those are present. Also tweak IntelliJ project file to be directory location independent.

r4912 | pcbrefugee | 2010-03-22 15:47:43 -0700 (Mon, 22 Mar 2010) | 1 line

adding externals for rebuilding PepC jar file

r4911 | pcbrefugee | 2010-03-22 14:19:40 -0700 (Mon, 22 Mar 2010) | 1 line

integrate PepC statistical peptide counting into TPP GUI (commandline version was added in commit 4886). Somewhat underdocumented at the moment, will add link to accompanying paper as soon as it becomes available.

r4888 | pcbrefugee | 2010-02-26 11:34:57 -0800 (Fri, 26 Feb 2010) | 1 line

[PepC] - some documentation tweaks

r4886 | pcbrefugee | 2010-02-25 15:58:56 -0800 (Thu, 25 Feb 2010) | 1 line

initial commit of "PepC: Proteomics software for identifying differentially expressed proteins based on spectral counting." developed by Insilicos with Lev Becker et al at the UW Heinecke lab (paper has been submitted to Bioinformatics). Changes for integration with Petunia will come in a different commit - what's here is sufficient for commandline usage.

r4877 | pcbrefugee | 2010-02-22 08:46:38 -0800 (Mon, 22 Feb 2010) | 1 line

properly escape FASTA protein descriptions containing reserved XML characters in pepXML output

r4856 | pcbrefugee | 2010-01-15 17:01:37 -0800 (Fri, 15 Jan 2010) | 1 line

[ProteoWizard] a handful more missed commits from recent ProteoWizard code reorg

r4855 | pcbrefugee | 2010-01-15 16:12:00 -0800 (Fri, 15 Jan 2010) | 1 line

[ProteoWizard] add a few things I missed from the most recent ProteoWizard code tree reorganization, update to ProteoWizard rev 1707

r4854 | pcbrefugee | 2010-01-15 14:44:15 -0800 (Fri, 15 Jan 2010) | 1 line

[proteowizard] sync up with proteowizard rev 1699, which includes my fix for reading mzXML files with nested scans (only affects TPP when reading mzXML without newlines, in which case RAMP passes off to pwiz).

r4852 | pcbrefugee | 2010-01-15 13:25:47 -0800 (Fri, 15 Jan 2010) | 1 line

[xinteract] skip the iprophet stuff for LabKey purposes (currently internally identified as "non interactive mode", which becomes a misnomer now, since this has nothing to do with interactivity and is a more general config issue)

r4851 | pcbrefugee | 2010-01-15 13:23:17 -0800 (Fri, 15 Jan 2010) | 1 line

[xtandem] No functional change, just a couple of standard include file adds/drops for crossplatform purposes, and identify the build as our own variant: VERSION "2009.10.01.1 (LabKey and ISB) " instead of just "2009.10.01.1".

r4814 | pcbrefugee | 2010-01-11 11:46:52 -0800 (Mon, 11 Jan 2010) | 1 line

[tpp_gui/win32] consistent use of single quotes so perl_paths build step can find and replace /usr/bin with windowsy default path

r4795 | pcbrefugee | 2009-12-14 08:38:47 -0800 (Mon, 14 Dec 2009) | 1 line

[mzXML] a copy of http://sashimi.sourceforge.net/schema_revision/mzXML_3.0/mzXML_3.0.xsd for convenience, it's surprisingly difficult to locate online if you don't know where to look already

r4793 | pcbrefugee | 2009-12-10 17:45:24 -0800 (Thu, 10 Dec 2009) | 1 line

[pwiz] silence some gcc 4.2.4 warnings about assigning string constant to non-const char *

r4792 | pcbrefugee | 2009-12-10 16:20:39 -0800 (Thu, 10 Dec 2009) | 1 line

[pwiz mzML reader code] sync up with ProteoWizard project at their rev 1608, for mzML CV version 2.29.0. Missed a handful of adds in previous commit.

r4790 | pcbrefugee | 2009-12-10 15:54:38 -0800 (Thu, 10 Dec 2009) | 1 line

[pwiz mzML reader code] sync up with ProteoWizard project at their rev 1608, for mzML CV version 2.29.0. Changes are not a drastic as length of commit list might seem to imply, much of that is just changes in header comments due to an author's change of institution

r4789 | pcbrefugee | 2009-12-10 12:18:32 -0800 (Thu, 10 Dec 2009) | 1 line

[ASAPRatio CGI] don't mistake "cidIndx" for "Indx" while parsing html field values, per user dctrud in https://mail.google.com/a/insilicos.com/#label/spctools-discuss/125795e322f2433b

r4788 | pcbrefugee | 2009-12-09 16:46:10 -0800 (Wed, 09 Dec 2009) | 1 line

[pwiz] tidy up the MSVC build for pwiz JNI bindings (no more win_lib), add a clean-pwiz_swig target to Makefile.pwiz.incl

r4787 | pcbrefugee | 2009-12-04 16:59:09 -0800 (Fri, 04 Dec 2009) | 1 line

[pwiz] create the java bindings output directory if need be

r4786 | pcbrefugee | 2009-12-04 16:54:12 -0800 (Fri, 04 Dec 2009) | 1 line

[pwiz] add an optional target "pwiz_swig" to generate JNI wrappers for pwiz's RAMPAdapter. Not actually used by TPP, but useful for other projects that use TPP components.

r4781 | pcbrefugee | 2009-11-24 09:28:39 -0800 (Tue, 24 Nov 2009) | 1 line

[MzXML2Search] tweak the usage statement, "-T" sets maximum MH+ mass, not "maximum MH+ scan".

r4780 | pcbrefugee | 2009-11-23 09:23:25 -0800 (Mon, 23 Nov 2009) | 1 line

[ProteinProphet] call to writeErrorAndSens is still needed even when running non-interactively, as in LabKey Server usage

r4776 | pcbrefugee | 2009-11-17 14:27:00 -0800 (Tue, 17 Nov 2009) | 1 line

[out2xml] add a cast (int)strlen for quiet compile

r4774 | pcbrefugee | 2009-11-16 11:58:31 -0800 (Mon, 16 Nov 2009) | 1 line

[xtandem] remove an unneeded (and, to some compilers, offensive) class declaration within class definition of the same

r4773 | pcbrefugee | 2009-11-16 10:36:32 -0800 (Mon, 16 Nov 2009) | 1 line

[windows build] tweak the readme to remove references to win_lib

r4761 | pcbrefugee | 2009-11-12 15:05:48 -0800 (Thu, 12 Nov 2009) | 32 lines

[xtandem] updates from labkey guys to get us at least partly up to date with GPM - see attachment in my email to spctools-dev of Nov 12 2009, the crucial part of which is copied here with total loss of formatting:

2. Details 2.1 Make TPP fork current (jeckels)

Item Change Justification 2.1.A mscore.cpp To mimic SEQUEST-like scoring, a scoring plugin has to modify the theoretical fragment ion series to adjust intensities and add appropriate neutral losses. To allow this make mscore::load_seq virtual under #ifdef PLUGGABLE_SCORING

2.2 Consider merging additional changes from GPM tree into TPP fork (jeckels) These are the changes in the current GPM sources that seem unrelated to our changes and relatively useful.

Item Change Justification

2.2.a tandem.cpp p3.cpp Current source code in the GPM has implements a round-robin allocation of work to threads that results in better balance of execution time between threads. Requested by Matt Fitzgibbon. Note the 2 files are almost identical, they compile under different flags

2.2.b mscore.cpp , GPM version at lines 530 and 1573 Current GPM builds have added support for including doubly charged y-ions in the scoring. This will raise some scores to make them more accurate. Requested by Matt Fitzgibbon.

2.2.c mscore.cpp Other changes in the GPM appear to be for compiler issues. E.g. surrounding a float literal with parenthesis. If we take all the changes in GPMs version the only different that remains will be the change from 2.1.A above.

2.2.d mpmods.cpp mprocess.cpp msequtilities.cpp GPM ads support for annotation files for enumerating possible mods Tags are refine, use annotations protein, use annotations GPM defaults to yes on both but we could default to no

2.2.e mscorepam.h GPM's mscorepam.h has a change with comment "WCH: wrong pair attribute checking"

r4751 | pcbrefugee | 2009-11-11 16:22:13 -0800 (Wed, 11 Nov 2009) | 1 line

[xinteract] when creating or running regression tests, ignore the WEBSERVER_TMP environment variable - tempfile use and the temporary renames that come with it whacks out the regression test files.

r4634 | pcbrefugee | 2009-09-23 14:49:57 -0700 (Wed, 23 Sep 2009) | 1 line

[installers] hunt down and remove any manual steps required to get all new and former pepXML and protXML schemas into the windows installer, and the *nix "make install"

r4625 | pcbrefugee | 2009-09-18 11:10:33 -0700 (Fri, 18 Sep 2009) | 1 line

[ProteinProphet] more informative error message when pepXML simply contains no analyses from peptideProphet (or interProphet, as appropriate)

r4618 | pcbrefugee | 2009-09-11 11:27:03 -0700 (Fri, 11 Sep 2009) | 1 line

[Mascot2XML] handle yet another title variant, example: "title=spectrumId=3774 Polarity=Positive ScanMode=MassScan TimeInSeconds=3710.73"

r4597 | pcbrefugee | 2009-08-31 14:11:34 -0700 (Mon, 31 Aug 2009) | 1 line

[xtandem / mzML 1.0 backward compatibility] - tweaks to pwiz RAMPAdapter to handle mzML 1.0 description of precursor ions

r4583 | pcbrefugee | 2009-08-18 17:50:33 -0700 (Tue, 18 Aug 2009) | 1 line

[plot-msms] deal with a signed/unsigned warning (with a probably unmeasurable performance improvement)

r4581 | pcbrefugee | 2009-08-18 17:20:33 -0700 (Tue, 18 Aug 2009) | 1 line

[xtandem] tandem's custom mzXML parser wasn't expecting compressionType="none"

r4580 | pcbrefugee | 2009-08-18 17:01:17 -0700 (Tue, 18 Aug 2009) | 1 line

[mzML reading] get current with pwiz 1.6 branch to fix a problem with reading WIFF-originated mzML files (was throwing an exception due to complicated nativeID, now we just use the index as scan number instead)

r4579 | pcbrefugee | 2009-08-18 13:11:08 -0700 (Tue, 18 Aug 2009) | 1 line

[amazon ec2 builds] add ubuntu 9.10 as a supported OS, using the 9.04 config scripts

r4578 | pcbrefugee | 2009-08-18 13:00:41 -0700 (Tue, 18 Aug 2009) | 1 line

[xtandem] tweak for building under GCC 4.4.0 (including fake stdint.h for win32 builds)

r4577 | pcbrefugee | 2009-08-18 12:25:21 -0700 (Tue, 18 Aug 2009) | 1 line

[perl scripts] use $FindBin::Bin to locate tpp_hostname executable

r4529 | pcbrefugee | 2009-08-05 15:08:55 -0700 (Wed, 05 Aug 2009) | 1 line

[indexmzXML] add this tool to the standard install, use RAMP interface to get 64 bit file pointers for proper indexing on win32

r4517 | pcbrefugee | 2009-08-04 14:07:39 -0700 (Tue, 04 Aug 2009) | 1 line

[pwiz build] add a couple of files which our use of RAMPAdapter doesn't actually require, but which are missed by some library managers as unresolved references

r4514 | pcbrefugee | 2009-08-04 10:00:35 -0700 (Tue, 04 Aug 2009) | 1 line

[mzML handling] cutting over to latest ProteoWizard code, to pick up mzML 1.1 capability (including mzML 1.0 read capability)

r4511 | pcbrefugee | 2009-08-03 13:36:34 -0700 (Mon, 03 Aug 2009) | 1 line

[fileDownloader.pl] tweak to make this compatible with the win32-specific perl_paths make step that removes hardcoded /usr/bin path to wget etc - no effect on linux usage

r4510 | pcbrefugee | 2009-08-03 12:55:41 -0700 (Mon, 03 Aug 2009) | 1 line

[mzML handling] update ProteoWizard external references to rev 1132, to include changes for mzML 1.0 read capability

r4508 | pcbrefugee | 2009-08-02 16:46:39 -0700 (Sun, 02 Aug 2009) | 1 line

[petunia] on win32, prepend full install path to commands (should help with .pl files as commands, which the win32 path mechanism doesn't know to search for)

r4502 | pcbrefugee | 2009-07-30 14:53:56 -0700 (Thu, 30 Jul 2009) | 1 line

[win32 installer] temp rename of README to README.txt while building installer allows windows to know how to display the readme doc at install time. Already did this for the MSVC installer build process, forgot about mingw.

David Shteynberg

RTCalc new tool for RT prediction

Out2XML: Use all of the last part of the encoded spectrum name for the charge not just one character, for multi character charge states

PepXMLViewer: Display only top ranked search_hit. Populate fields with search scores from any of the engines used in the analysis (useful for iProphet viewing).

ASAPRatio: changes to display ratios of secondary proteins from protein groups. TODO: Next and Prev Protein buttons will take you to the next protein group not the next protein in the group, should be corrected or disabled.

PeptideProphetParser: Replace SSRCalc with RTCalc for retention time modelling.

RefreshParser: Only map unrejected peptides.

ASAPRatio: changes to display ratios of secondary proteins from protein groups.

PeptideProphetParser: Using ppm in the accurate mass model

PeptideProphetParser: Report error and don't model spectra with assumed_charge not equal to encoded charge in the name. Fix bug reported by Ludovic.

InteractParser: Make sure to not strip out the enzyme info when not specified on commandline.

InteractParser: BUGFIX prevent double delete of tag pointer.

InteractParser: Fix crash when -E option is not specified.

Tandem2XML: Handle multiple variable mods on same AA

RefreshParser: report the prev_aa and next_aa for top NTT match in the protein, not just the first entry. Test that db defn line actually has a '|' before testing if it comes before a ' '.

InteractParser: When an enzyme is given on the commandline overwrite the current sample_enzyme tag with the enzyme specified, old behaviour introduced competing sample_enzyme tags creating an inconsistency under certain conditions of use.

InterProphetParser - better usage statement, new option to output only peptides above a certain probability value.

InterProphetParser - adding computation of observed fits among initially low and high probability results, using variable bandwidths from the modeled fits.

ProteinProphet Store a separate value with peptide's total weight in the protein group.

PeptideProphetParser: Adding InspectFvalue, PHOSPHO model, TOPCAT model.

xinteract PHOSPHO model and enable option InteractParser -P for correcting protein names in omssa output.

PeptideProphetParser new PHOSPHO model. Check all matching proteins for a peptide and count it as decoy only if all are decoys. Tuning max reward parameters for ACCMASS model. Print warning if not decoys are found. Count decoys and forward PSMs found. PeptideProphetParser new PHOSPHO model. Also fix the output when there are multiple top_hits so the probability is reported with the top most hit.

InterProphetParser Compute and report observed distributions in addition to the modeled distributions already reported.

InterProphetParser Filter out any old iProphet results from the final output file.

InterProphetParser Compute and report observed distributions in addition to the modeled distributions already reported.

ProteinProphet store peptide group weight (sum of peptide's weight in the protein group) separatelly from peptide's weight in the protein.

PeptideProphetParser tuning params on Tandem's semi-parametric model

PeptideProphetParser Inspect f-value model.

PeptideProphetParser adjusting Myrimatch f-value params.

PeptideProphetParser tweaking the discriminant function params for OMSSA analysis

Caching variable bandwidth for quicker runtime. New function varBWdensityFit now can also take an additional parameter of a pointer to a Fit object.

PeptideProphetParser now stores all proteins matched by a search result.

ASAPRATIO: Bug Fix, wrong masses were being computed for charge 5+, now corrected.

ASAPCGIDisplay.cgi: BUG FIX Normalized Ratio was not getting displayed.

PeptideProphet: Fixing seg fault appearing in MALDI mode on PROBID results.

RefreshParser: Bug fix with UNMAPPED peptides not showing up UNMAPPED under some conditions. Use minimum number of enzymatic termini from the search_hit num_tol_term attribute.

[ProteinProphet] Fix bug of indistinguishable_peptides being reported wrong with bad charge and first 2 chars stripped off.

[PeptideProphetParser] Make tool more robust by auto trimming whitespace from spectrum names. Tandem searches submitted by Scott Stansfield (Aug 2009) where generated with method mzXML->mgf->tandem->pepXML was adding an extra space to the end of spectrum name. This commit addresses the issue with Scott's data.

[InteractParser] Fix seg fault bug when dbtype option is set -T

henrylam

SpectraST

New features (SpectraST v.4.0)
- ETD support
- iProphet support
- Artificial decoy spectrum generation (-cAD, -cc, -cy options. Ref. Lam et al., J. Proteome Res. 9, 605-610 (2010))
- MRM transition list generation (-cM option. Ref. Sherwood et al., J. Proteome Res. 8, 4396-4405 (2009))
- User-defined modifications (-M option)
- Semi-empirical spectrum generation based on user-specified modifications (-cAM, -cx options)
- Searching MGF (Mascot Generic Format) files
- Clickable (HTML) search output format
- Gzipped (.gz) file support
- Non-peptide and unidentified entries
- Combining libraries by appending (-cJA option)
- Searching all charges (ignore specified query charge state) (-sz option)
- Lib2HTML option to display by sorted precursor m/z
- "Butterfly" plot for two library spectra using plotspectrast
- Several other advanced options

Other changes and bug fixes
- Modernized library statistics reporting to stdout and in .pepidx file
- Better book-keeping: fragmentation method, precursor intensity, and collision energy stored with library spectra
- Improved annotation algorithm
- Various bug fixes

calctppstats.pl

Option to specify probability or FDR threshold
Option to count number of unique proteins mapped to by PSMs

xinteract

Allow specification of protein database for RefreshParser (and hence for ProteinProphet) by -D option (in case that information is not in the pepXML file).
Skip RefreshParser, rather than crashing, if the database is not specified or not found.

eng_jk

XPRESS

Added support for intensity ratios (versus area based ratios) and specifying negative mass offsets. XPRESS includes better support for highres data by optionally summing individual isotope peaks for chromatogram reconstruction.

Added minimum chromatrogram ion count parameter -c<num>. This parameter filters out entries from being quantified unless the reconstruction chromatogram meets the minimum number of peaks specified.

Added -l label free option. This option will calculate stats on precursor ions only. Resulting analysis is labeled as 'xpresslabelfree' in pep.xml.

MzXML2Search

Add -N option to print out top N most intense peaks in a spectrum. Needed for large peaklists from new instrument as Mascot will complain if input peak list exceeds 10,000 count.

zhisun

r4784 | zhisun | 2009-11-30 13:02:05 -0800 (Mon, 30 Nov 2009) | 1 line

Chris Paulse modified the script and made it more permissive regarding the precursorCharge target string (doesn’t expect space immediately after the close quote.)

r4545 | zhisun | 2009-08-07 15:02:14 -0700 (Fri, 07 Aug 2009) | 1 line

solve memory problem

Full Integration of MaRiMba

Completion of the full integration of MaRiMba into the TPP.

spacepod

r4972 | spacepod | 2010-05-10 12:24:18 -0700 (Mon, 10 May 2010) | 2 lines

[build process] 1) add dectection for 64-bit OS X systems; 2) use macports vs fink search paths for extra libraries (can add detection, if requested)

r4971 | spacepod | 2010-05-10 12:21:03 -0700 (Mon, 10 May 2010) | 2 lines

[PepXMLViewer] adding casts to work under boost 1.43.0

r4967 | spacepod | 2010-05-04 17:20:10 -0700 (Tue, 04 May 2010) | 2 lines

[ASAPRatioPeptideParser] adding experimental wavelet smoothing. Test using new ASAPRatioPeptideParser -w option. From WaveletQuant implmentation, http://www.biomedcentral.com/1471-2105/11/219

r4922 | spacepod | 2010-03-31 16:21:57 -0700 (Wed, 31 Mar 2010) | 2 lines

[Makefile] removing extra tab character

r4921 | spacepod | 2010-03-31 11:53:14 -0700 (Wed, 31 Mar 2010) | 2 lines

[linux install] generalizing ubuntu 9.04 install to 9.10 as well (tested)

r4872 | spacepod | 2010-02-10 16:19:05 -0800 (Wed, 10 Feb 2010) | 1 line

[OS requirements] updating ubuntu 8.10 install

r4785 | spacepod | 2009-11-30 17:46:38 -0800 (Mon, 30 Nov 2009) | 1 line

[mingw build] updates for mingw build

r4660 | spacepod | 2009-09-28 14:17:22 -0700 (Mon, 28 Sep 2009) | 3 lines

[c to c++ cleanup] catching a few files that svn got confused on the first time.

r4659 | spacepod | 2009-09-28 14:07:53 -0700 (Mon, 28 Sep 2009) | 3 lines

[c to c++ cleanup] catching a few files that svn got confused on the first time.

r4658 | spacepod | 2009-09-28 14:02:07 -0700 (Mon, 28 Sep 2009) | 3 lines

[c to c++ cleanup] catching a few files that svn got confused on the first time.

r4657 | spacepod | 2009-09-28 13:44:33 -0700 (Mon, 28 Sep 2009) | 4 lines

[c to c++ rename] merging changes to convert file extensions and build process from c to c++, from cpprename. fully tested in 'cpprename' branch.

r4656 | spacepod | 2009-09-28 13:19:44 -0700 (Mon, 28 Sep 2009) | 1 line

[windows builds] updating paths for boost, expat dependencies; from cpprename branch

r4655 | spacepod | 2009-09-28 12:25:19 -0700 (Mon, 28 Sep 2009) | 1 line

[restoring trunk/tpp to cleaner history, before c->c++ thrashing

r4587 | spacepod | 2009-08-24 12:13:54 -0700 (Mon, 24 Aug 2009) | 1 line

[mingw build] adding script for building TPP under mingw, so that it's easier to get this going from outside the mingw/msys environment.

r4573 | spacepod | 2009-08-13 17:48:57 -0700 (Thu, 13 Aug 2009) | 1 line